Alignments for a candidate for hisD in Thermomonospora curvata DSM 43183

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisD in Thermomonospora curvata DSM 43183

Align Histidinol dehydrogenase; HDH; EC 1.1.1.23 (characterized)
to candidate WP_012853226.1 TCUR_RS14290 histidinol dehydrogenase

Query= SwissProt::P9WNW9
         (444 letters)



>NCBI__GCF_000024385.1:WP_012853226.1
          Length = 435

 Score =  548 bits (1413), Expect = e-160
 Identities = 287/436 (65%), Positives = 338/436 (77%), Gaps = 7/436 (1%)

Query: 7   VLTRIDLRGAELTAAELRAALPRGGADVEAVLPTVRPIVAAVAERGAEAALDFGASFDGV 66
           +++RIDLRG+     +LR+ LPR   DVEA L  VRPI   V  RGA A  ++   FDGV
Sbjct: 1   MISRIDLRGS--LPGDLRSVLPRAELDVEAALERVRPICEDVRHRGAAAVREYTKKFDGV 58

Query: 67  RPHAIRVPDAALDAALAGLDCDVCEALQVMVERTRAVHSGQRRTDVTTTLGPGATVTERW 126
              ++RVP AAL+ ALAGLD  V +AL+  + R R VH  QRRTDVTT + PG TVTERW
Sbjct: 59  ELESLRVPAAALERALAGLDPAVRDALEESIRRARLVHRDQRRTDVTTQVVPGGTVTERW 118

Query: 127 VPVERVGLYVPGGNAVYPSSVVMNVVPAQAAGVDSLVVASPPQAQWDGMPHPTILAAARL 186
           +PVERVGLYVPGG AVYPSSVVMNVVPAQ AGV SL V SPPQ ++ G+PHP ILAA  L
Sbjct: 119 IPVERVGLYVPGGRAVYPSSVVMNVVPAQEAGVGSLAVTSPPQQEFGGLPHPAILAACAL 178

Query: 187 LGVDEVWAVGGAQAVALLAYGGTDTDGAALTPVDMITGPGNIYVTAAKRLCRSRVGIDAE 246
           LGV+EV+A GGAQ++A+LAYG  +       PV+++TGPGNI+V AAKR  R  VGID+E
Sbjct: 179 LGVEEVYAAGGAQSIAMLAYGTDEC-----RPVNLVTGPGNIWVAAAKRHLRGVVGIDSE 233

Query: 247 AGPTEIAILADHTADPVHVAADLISQAEHDELAASVLVTPSEDLADATDAELAGQLQTTV 306
           AGPTEIAILAD +ADPVHVAADLISQAEHD LAA+VLVT SE+LA+  + ELA Q+  T 
Sbjct: 234 AGPTEIAILADASADPVHVAADLISQAEHDTLAAAVLVTDSEELAERVERELAEQVARTK 293

Query: 307 HRERVTAALTGRQSAIVLVDDVDAAVLVVNAYAAEHLEIQTADAPQVASRIRSAGAIFVG 366
           H ER+T AL GRQS IVLVDD++A + VVNAYAAEHLEIQTA+A QVA R+R+AGAIF+G
Sbjct: 294 HTERITQALAGRQSGIVLVDDIEAGLAVVNAYAAEHLEIQTANARQVAERVRNAGAIFIG 353

Query: 367 PWSPVSLGDYCAGSNHVLPTAGCARHSSGLSVQTFLRGIHVVEYTEAALKDVSGHVITLA 426
           P SPVSLGDY AGSNHVLPT GCA HSSGLSVQ+FLRG+HVVEY  AAL + +  V+ LA
Sbjct: 354 PHSPVSLGDYLAGSNHVLPTGGCACHSSGLSVQSFLRGVHVVEYDRAALAEATARVVALA 413

Query: 427 TAEDLPAHGEAVRRRF 442
            AEDLPAHG A++ RF
Sbjct: 414 EAEDLPAHGAAMKARF 429


Lambda     K      H
   0.317    0.132    0.383 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 540
Number of extensions: 19
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 444
Length of database: 435
Length adjustment: 32
Effective length of query: 412
Effective length of database: 403
Effective search space:   166036
Effective search space used:   166036
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate WP_012853226.1 TCUR_RS14290 (histidinol dehydrogenase)
to HMM TIGR00069 (hisD: histidinol dehydrogenase (EC 1.1.1.23))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR00069.hmm
# target sequence database:        /tmp/gapView.30803.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00069  [M=393]
Accession:   TIGR00069
Description: hisD: histidinol dehydrogenase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                                 Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   8.6e-149  481.9   5.3   9.7e-149  481.8   5.3    1.0  1  lcl|NCBI__GCF_000024385.1:WP_012853226.1  TCUR_RS14290 histidinol dehydrog


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000024385.1:WP_012853226.1  TCUR_RS14290 histidinol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  481.8   5.3  9.7e-149  9.7e-149       1     393 []      33     428 ..      33     428 .. 0.99

  Alignments for each domain:
  == domain 1  score: 481.8 bits;  conditional E-value: 9.7e-149
                                 TIGR00069   1 vkeiiedvrkeGdeAlleytekfdkvkleslrvseeeleealeavdeelkealelaaeniekfhekqlp 69 
                                               v++i+edvr++G +A++eyt+kfd+v+leslrv+++ le+al+ +d+++++ale+++++ + +h++q++
  lcl|NCBI__GCF_000024385.1:WP_012853226.1  33 VRPICEDVRHRGAAAVREYTKKFDGVELESLRVPAAALERALAGLDPAVRDALEESIRRARLVHRDQRR 101
                                               799****************************************************************** PP

                                 TIGR00069  70 esveveteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPpkk..dgkvnp 136
                                               ++v+++  +g ++++++ p+ervglYvPgG+a ypS+v+m++vpA+ Agv +++v++Pp++   g  +p
  lcl|NCBI__GCF_000024385.1:WP_012853226.1 102 TDVTTQVVPGGTVTERWIPVERVGLYVPGGRAVYPSSVVMNVVPAQEAGVGSLAVTSPPQQefGGLPHP 170
                                               ***********************************************************87445789** PP

                                 TIGR00069 137 avlaaakllgvdevykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvfgevgidmiaGPsEv 205
                                               a+laa++llgv+evy++GGaq+ia+layGt+++++v+ ++GPGni+V+aAK+++ g vgid+ aGP+E+
  lcl|NCBI__GCF_000024385.1:WP_012853226.1 171 AILAACALLGVEEVYAAGGAQSIAMLAYGTDECRPVNLVTGPGNIWVAAAKRHLRGVVGIDSEAGPTEI 239
                                               ********************************************************************* PP

                                 TIGR00069 206 lviadesanpelvaaDllsqaEHdedaqailvttseelaekveeeveeqleelerkeiaekslek.nga 273
                                               +++ad+sa+p +vaaDl+sqaEHd+ a+a+lvt+seelae+ve+e++eq+++++++e ++++l+  ++ 
  lcl|NCBI__GCF_000024385.1:WP_012853226.1 240 AILADASADPVHVAADLISQAEHDTLAAAVLVTDSEELAERVERELAEQVARTKHTERITQALAGrQSG 308
                                               *********************************************************999999976899 PP

                                 TIGR00069 274 iilvddleealelsneyApEHLelqtkdpeellkkiknaGsvflGeytpealgdyvaGpnhvLPTsgtA 342
                                               i+lvdd+e  l+++n+yA+EHLe+qt+++++++++++naG++f+G+++p++lgdy+aG+nhvLPT+g+A
  lcl|NCBI__GCF_000024385.1:WP_012853226.1 309 IVLVDDIEAGLAVVNAYAAEHLEIQTANARQVAERVRNAGAIFIGPHSPVSLGDYLAGSNHVLPTGGCA 377
                                               ********************************************************************* PP

                                 TIGR00069 343 rfasglsvedFlkrisvqelskealeelaeaveklaeaEgLeaHaeavevR 393
                                                ++sglsv++Fl+ ++v+e++++al+e    v++laeaE+L aH +a+++R
  lcl|NCBI__GCF_000024385.1:WP_012853226.1 378 CHSSGLSVQSFLRGVHVVEYDRAALAEATARVVALAEAEDLPAHGAAMKAR 428
                                               ************************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (393 nodes)
Target sequences:                          1  (435 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 10.94
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for Amino acid biosynthesis